When transforming emails into FootPrints records, I noticed that email from a few distinct email senders is being stripped of carriage returns. The only difference between the two examples below is that the offending email is being redirected via an smtp service (smtp.com). Is there any way to mitigate this issue?

Unfortunately I don't have access to the server back-end to collect debug logs. Historically, have you ever come across a similar issue and was it easily resolved, or did it have to go to development to fix?

I haven't seen this before. If you don't have access to the server, you could still enable debugging and then send yourself the error report under Admin|System|Logs|Send Error Report. Just change the to address to your own and check the box to send the email debugging.